8PIS | pdb_00008pis

Crystal structure of Ser33 in complex with L-Serine

PDB DOI: https://doi.org/10.2210/pdb8PIS/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-22 Released: 2025-01-15
Deposition Author(s): Perrone, S., Cifuente, J.O., Marina, A., Mastrella, L., Trastoy, B., Linster, C.L., Guerin, M.E.
Funding Organization(s): Ministry of Economy and Competitiveness (MINECO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.216 (Depositor), 0.214 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Ser33 in complex with L-Serine

Perrone, S., Cifuente, J.O., Marina, A., Mastrella, L., Trastoy, B., Linster, C.L., Guerin, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 425.22 kDa
Atom Count: 26,154
Modeled Residue Count: 3,493
Deposited Residue Count: 3,864
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoglycerate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	473	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SER33 EC: 1.1.1.399 (UniProt), 1.1.1.95 (UniProt)
UniProt
Find proteins for P40510 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40510 Go to UniProtKB: P40510
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40510
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoglycerate dehydrogenase	I J K L [auth M] M [auth N] I, J, K, L [auth M], M [auth N], N [auth O], O [auth Q], P [auth L]	10	Saccharomyces cerevisiae	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E]	BA [auth F] CA [auth G] EA [auth H] Q [auth A] S [auth B] BA [auth F], CA [auth G], EA [auth H], Q [auth A], S [auth B], U [auth C], W [auth D], Y [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain R [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] DA [auth G] FA [auth H] R [auth A] T [auth B] AA [auth E], DA [auth G], FA [auth H], R [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]